Autoimmune thyroid diseases (AITD) and type 1 diabetes (T1D) frequently occur within the same family and in the same individual. When AITD+T1D occur in the same individual, the phenotype is considered a variant of the polyglandular syndrome type 3 (APS3 variant [APS3v]). Our goals are: (1) to identify and characterize the joint susceptibility genes for AITD and T1D, and (2) to dissect the mechanisms by which they cause disease. During the last grant period, we have made substantial progress toward these goals, including: (1) We completed the first reported genome scan in families with AITD & T1D, mapped new loci common to AITD & T1D, and identified 3 joint genes for AITD & T1D in linked loci; (2)Determined thatCTLA-4, PTPN22, Insulin VNTR are susceptibility genes for the APS3v (AITD+T1D) phenotype; (3) Discovered a unique HLA-DR pocket amino acid signature that was critical for the development of APS3v and determined the 3-D structure of that pocket; (4) Assembled a dataset of ~ 700 individuals with AITD+T1D (APS3v), giving us power for large scale association studies in this subset; and (5) Dissected mechanisms by which variants in AITD genes (Tg, CD40, & TSHR) predispose to disease. We propose to build on these findings to pursue our hypothesis that the joint etiology of AITD & T1D depends on genetic and biological interactions between several genes. Our specific aims are: Specific Aim 1: To identify & characterize thyroglobulin (Tg), TPO, insulin, and GAD65 peptides that bind to the unique HLA-DR pocket that we found to be critical for the development of APS3v. We will use: (1) molecular modeling and bioinformatics studies to predict peptides that best fit the structure of the APS3v-associated pocket; and (2) biochemical and mass spectrometry experiments to identify peptides that bind to the pocket. Specific Aim 2: To dissect the mechanisms by which CTLA-4 & FOXP3 variants predispose to APS3v: (1) CTLA-4: we will test whether a 3'UTR microsatellite predisposes to APS3v by lowering CTLA-4 mRNA stability. (2) FOXP3: we will examine whether an intron 5 (TC)n microsatellite repeat confers risk for APS3v by altering the alternative splicing of FOXP3. Specific Aim 3: To fine map and identify new susceptibility genes for APS3v (AITD+T1D): (1) Fine mapping: A major locus on 2p will be fine mapped using densely spaced SNPs & the gene identified. (2) Subset analysis: We will perform a comprehensive association study on the subset of APS3v patients, using our large dataset of APS3v patients and available genotypes on 4000 ethnically matched controls. (3) Gene-gene interaction: genes identified will be analyzed for gene-gene interaction. The current proposal builds directly on the knowledge gained in the previous grant period, and aims to dissect the molecular pathways causing the strong association between AITD and T1D. This will lead to better understanding of the common etiology of both AITD & T1D, as well as APS3v, and may facilitate the development of mechanism- based treatment modalities, such as HLA-DR pocket blockade, or CTLA-4 activation. PUBLIC HEALTH RELEVANCE: Autoimmune thyroid diseases, including Hashimoto's thyroiditis and Graves' disease commonly occur together with type 1 (Juvenile) diabetes in the same families and in the same individual, most likely due to shared genetic susceptibility. The goal of our studies is to identify and characterize the joint susceptibility genes for autoimmune thyroid diseases and type 1 diabetes, and to study the mechanisms by which they cause these two diseases. Understanding the mechanisms causing the strong association between thyroid autoimmunity and type1 diabetes will allow us not only disease predictions within families, but also to develop rational, mechanism-based, treatment and prevention strategies